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Magnesium in PDB 1g9z: Laglidadg Homing Endonuclease I-Crei / Dna Product Complex with Magnesium

Protein crystallography data

The structure of Laglidadg Homing Endonuclease I-Crei / Dna Product Complex with Magnesium, PDB code: 1g9z was solved by B.Chevalier, R.J.Monnat, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.92 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.000, 67.900, 88.300, 90.00, 91.60, 90.00
R / Rfree (%) 20.4 / 24.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Laglidadg Homing Endonuclease I-Crei / Dna Product Complex with Magnesium (pdb code 1g9z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Laglidadg Homing Endonuclease I-Crei / Dna Product Complex with Magnesium, PDB code: 1g9z:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 1g9z

Go back to Magnesium Binding Sites List in 1g9z
Magnesium binding site 1 out of 3 in the Laglidadg Homing Endonuclease I-Crei / Dna Product Complex with Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Laglidadg Homing Endonuclease I-Crei / Dna Product Complex with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg902

b:15.3
occ:1.00
OD1 B:ASP220 2.0 18.5 1.0
OD1 A:ASP20 2.0 15.6 1.0
OP2 D:DG515 2.0 18.3 0.5
OP1 F:DG615 2.1 9.5 0.5
O3' E:DC614 2.4 9.8 0.5
O3' C:DA514 2.4 12.2 0.5
CG B:ASP220 3.1 16.2 1.0
CG A:ASP20 3.2 12.1 1.0
P D:DG515 3.3 19.1 0.5
C3' C:DA514 3.4 11.2 0.5
P F:DG615 3.4 15.1 0.5
C3' E:DC614 3.5 12.3 0.5
MG F:MG903 3.6 14.8 1.0
OD2 B:ASP220 3.7 17.1 1.0
OD2 A:ASP20 3.7 15.4 1.0
O5' F:DG615 3.7 9.6 0.5
MG D:MG901 3.8 16.6 1.0
O5' D:DG515 3.8 18.3 0.5
O A:GLY19 3.8 12.3 1.0
C4' C:DA514 3.9 14.1 0.5
O B:GLY219 3.9 13.4 1.0
OP1 D:DG515 3.9 18.5 0.5
OP3 F:DG615 4.1 10.9 0.5
O D:HOH33 4.1 24.9 1.0
O F:HOH9 4.2 19.3 1.0
C4' E:DC614 4.3 19.5 0.5
CB B:ASP220 4.4 14.8 1.0
CB A:ASP20 4.4 10.0 1.0
C A:GLY19 4.5 11.8 1.0
C B:GLY219 4.5 16.1 1.0
CA A:ASP20 4.5 10.2 1.0
OP1 C:DA514 4.5 7.8 0.5
CA B:ASP220 4.5 12.7 1.0
OP3 D:DG515 4.5 22.8 0.5
OP2 F:DG615 4.6 8.0 0.5
C2' E:DC614 4.6 9.3 0.5
OP1 E:DC614 4.7 7.8 0.5
C2' C:DA514 4.7 11.7 0.5
N B:ASP220 4.8 13.1 1.0
N A:ASP20 4.8 12.7 1.0
C5' C:DA514 4.8 12.8 0.5
O4' C:DA514 4.9 20.1 0.5

Magnesium binding site 2 out of 3 in 1g9z

Go back to Magnesium Binding Sites List in 1g9z
Magnesium binding site 2 out of 3 in the Laglidadg Homing Endonuclease I-Crei / Dna Product Complex with Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Laglidadg Homing Endonuclease I-Crei / Dna Product Complex with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg901

b:16.6
occ:1.00
OP1 E:DC614 1.9 7.8 0.5
OD2 B:ASP220 2.0 17.1 1.0
O A:GLY19 2.1 12.3 1.0
O A:HOH154 2.1 15.8 1.0
OP2 D:DG515 2.3 18.3 0.5
OP3 D:DG515 2.4 22.8 0.5
P D:DG515 2.8 19.1 0.5
CG B:ASP220 3.0 16.2 1.0
C A:GLY19 3.1 11.8 1.0
OD1 B:ASP220 3.3 18.5 1.0
P E:DC614 3.4 15.4 0.5
CA A:GLY19 3.6 11.0 1.0
MG C:MG902 3.8 15.3 1.0
O D:HOH29 3.9 24.9 1.0
O5' D:DG515 3.9 18.3 0.5
O5' E:DC614 4.0 18.1 0.5
O3' E:DA613 4.1 19.9 0.5
NE2 B:GLN247 4.1 14.1 1.0
OP1 D:DG515 4.1 18.5 0.5
O A:ASP18 4.2 15.7 1.0
OE1 B:GLN247 4.2 20.1 1.0
OD1 A:ASP20 4.3 15.6 1.0
N A:ASP20 4.3 12.7 1.0
CB B:ASP220 4.4 14.8 1.0
OP2 E:DC614 4.4 13.8 0.5
C5' D:DG515 4.5 19.5 0.5
CD B:GLN247 4.6 16.1 1.0
C4' E:DC614 4.6 19.5 0.5
O3' E:DC614 4.6 9.8 0.5
CA A:ASP20 4.7 10.2 1.0
N A:GLY19 4.8 13.7 1.0
C3' E:DC614 4.8 12.3 0.5
O A:HOH167 4.8 32.0 1.0
O3' C:DA514 4.8 12.2 0.5
C A:ASP18 4.9 14.5 1.0
C5' E:DC614 4.9 29.0 0.5

Magnesium binding site 3 out of 3 in 1g9z

Go back to Magnesium Binding Sites List in 1g9z
Magnesium binding site 3 out of 3 in the Laglidadg Homing Endonuclease I-Crei / Dna Product Complex with Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Laglidadg Homing Endonuclease I-Crei / Dna Product Complex with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg903

b:14.8
occ:1.00
OD2 A:ASP20 2.0 15.4 1.0
OP1 C:DA514 2.0 7.8 0.5
O B:GLY219 2.1 13.4 1.0
O B:HOH355 2.2 15.6 1.0
OP1 F:DG615 2.2 9.5 0.5
OP2 F:DG615 2.4 8.0 0.5
P F:DG615 2.7 15.1 0.5
CG A:ASP20 2.9 12.1 1.0
C B:GLY219 3.1 16.1 1.0
OD1 A:ASP20 3.2 15.6 1.0
P C:DA514 3.5 11.7 0.5
MG C:MG902 3.6 15.3 1.0
CA B:GLY219 3.7 14.9 1.0
O5' F:DG615 3.7 9.6 0.5
O F:HOH21 3.9 23.9 1.0
O3' C:DG513 4.0 10.4 0.5
OP3 F:DG615 4.0 10.9 0.5
OD1 B:ASP220 4.1 18.5 1.0
NE2 A:GLN47 4.1 11.9 1.0
O B:ASP218 4.1 11.1 1.0
OE1 A:GLN47 4.2 8.4 1.0
N B:ASP220 4.3 13.1 1.0
C5' C:DA514 4.3 12.8 0.5
CB A:ASP20 4.3 10.0 1.0
C4' C:DA514 4.4 14.1 0.5
OP2 C:DA514 4.4 8.3 0.5
O5' C:DA514 4.4 7.9 0.5
C5' F:DG615 4.4 8.1 0.5
CD A:GLN47 4.6 10.9 1.0
CA B:ASP220 4.7 12.7 1.0
N B:GLY219 4.8 11.3 1.0
O3' C:DA514 4.9 12.2 0.5
O B:HOH387 4.9 26.9 1.0
C B:ASP218 4.9 14.4 1.0
C3' C:DA514 5.0 11.2 0.5

Reference:

B.S.Chevalier, R.J.Monnat Jr., B.L.Stoddard. The Homing Endonuclease I-Crei Uses Three Metals, One of Which Is Shared Between the Two Active Sites. Nat.Struct.Biol. V. 8 312 2001.
ISSN: ISSN 1072-8368
PubMed: 11276249
DOI: 10.1038/86181
Page generated: Mon Dec 14 05:57:41 2020

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